HEADER NEUROPEPTIDE 10-APR-23 8SEJ TITLE TYPE I BETA-AMYLOID 42 FILAMENTS FROM DOWN SYNDROME COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PROTEIN 42; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J; COMPND 4 OTHER_DETAILS: TYPE I BETA-AMYLOID 42 FILAMENTS FROM DOWN SYNDROME COMPND 5 CASE 2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS BETA AMYLOID FILAMENTS, DOWN SYNDROME, NEUROPEPTIDE, HUMAN TRISOMY 21 EXPDTA ELECTRON MICROSCOPY AUTHOR M.R.HOQ,S.R.BHARATH,F.S.VAGO,W.JIANG REVDAT 2 10-APR-24 8SEJ 1 JRNL REVDAT 1 03-APR-24 8SEJ 0 JRNL AUTH A.FERNANDEZ,M.R.HOQ,G.I.HALLINAN,D.LI,S.R.BHARATH,F.S.VAGO, JRNL AUTH 2 X.ZHANG,K.A.OZCAN,K.L.NEWELL,H.J.GARRINGER,W.JIANG,B.GHETTI, JRNL AUTH 3 R.VIDAL JRNL TITL CRYO-EM STRUCTURES OF AMYLOID-BETA AND TAU FILAMENTS IN DOWN JRNL TITL 2 SYNDROME. JRNL REF NAT.STRUCT.MOL.BIOL. 2024 JRNL REFN ESSN 1545-9985 JRNL PMID 38553642 JRNL DOI 10.1038/S41594-024-01252-3 REMARK 2 REMARK 2 RESOLUTION. 3.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFFIND REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.170 REMARK 3 NUMBER OF PARTICLES : 45575 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8SEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273261. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : TYPE I BETA AMYLOID 42 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.20 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5046.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 81000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 27 CB ASN A 27 CG -0.212 REMARK 500 VAL A 40 CB VAL A 40 CG2 -0.135 REMARK 500 ASN B 27 CB ASN B 27 CG -0.212 REMARK 500 VAL B 40 CB VAL B 40 CG2 -0.135 REMARK 500 ASN C 27 CB ASN C 27 CG -0.213 REMARK 500 VAL C 40 CB VAL C 40 CG2 -0.135 REMARK 500 ASN D 27 CB ASN D 27 CG -0.213 REMARK 500 VAL D 40 CB VAL D 40 CG2 -0.136 REMARK 500 ASN E 27 CB ASN E 27 CG -0.213 REMARK 500 VAL E 40 CB VAL E 40 CG2 -0.135 REMARK 500 ASN F 27 CB ASN F 27 CG -0.213 REMARK 500 VAL F 40 CB VAL F 40 CG2 -0.135 REMARK 500 ASN G 27 CB ASN G 27 CG -0.213 REMARK 500 VAL G 40 CB VAL G 40 CG2 -0.135 REMARK 500 ASN H 27 CB ASN H 27 CG -0.212 REMARK 500 VAL H 40 CB VAL H 40 CG2 -0.135 REMARK 500 ASN I 27 CB ASN I 27 CG -0.212 REMARK 500 VAL I 40 CB VAL I 40 CG2 -0.134 REMARK 500 ASN J 27 CB ASN J 27 CG -0.213 REMARK 500 VAL J 40 CB VAL J 40 CG2 -0.136 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-40416 RELATED DB: EMDB REMARK 900 TYPE I BETA-AMYLOID 42 FILAMENTS FROM DOWN SYNDROME DBREF 8SEJ A 9 42 UNP P05067 A4_HUMAN 680 713 DBREF 8SEJ B 9 42 UNP P05067 A4_HUMAN 680 713 DBREF 8SEJ C 9 42 UNP P05067 A4_HUMAN 680 713 DBREF 8SEJ D 9 42 UNP P05067 A4_HUMAN 680 713 DBREF 8SEJ E 9 42 UNP P05067 A4_HUMAN 680 713 DBREF 8SEJ F 9 42 UNP P05067 A4_HUMAN 680 713 DBREF 8SEJ G 9 42 UNP P05067 A4_HUMAN 680 713 DBREF 8SEJ H 9 42 UNP P05067 A4_HUMAN 680 713 DBREF 8SEJ I 9 42 UNP P05067 A4_HUMAN 680 713 DBREF 8SEJ J 9 42 UNP P05067 A4_HUMAN 680 713 SEQRES 1 A 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 A 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 A 34 MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 B 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 B 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 B 34 MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 C 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 C 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 C 34 MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 D 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 D 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 D 34 MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 E 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 E 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 E 34 MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 F 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 F 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 F 34 MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 G 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 G 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 G 34 MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 H 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 H 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 H 34 MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 I 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 I 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 I 34 MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 J 34 GLY TYR GLU VAL HIS HIS GLN LYS LEU VAL PHE PHE ALA SEQRES 2 J 34 GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU SEQRES 3 J 34 MET VAL GLY GLY VAL VAL ILE ALA SHEET 1 AA1 5 TYR A 10 HIS A 13 0 SHEET 2 AA1 5 TYR C 10 HIS C 13 1 O HIS C 13 N VAL A 12 SHEET 3 AA1 5 TYR E 10 HIS E 13 1 O HIS E 13 N VAL C 12 SHEET 4 AA1 5 TYR G 10 HIS G 13 1 O HIS G 13 N VAL E 12 SHEET 5 AA1 5 TYR I 10 HIS I 13 1 O HIS I 13 N VAL G 12 SHEET 1 AA2 5 LYS A 16 PHE A 20 0 SHEET 2 AA2 5 LYS C 16 PHE C 20 1 O PHE C 19 N PHE A 20 SHEET 3 AA2 5 LYS E 16 PHE E 20 1 O PHE E 19 N PHE C 20 SHEET 4 AA2 5 LYS G 16 PHE G 20 1 O PHE G 19 N PHE E 20 SHEET 5 AA2 5 LYS I 16 PHE I 20 1 O PHE I 19 N PHE G 20 SHEET 1 AA3 5 VAL A 24 GLY A 25 0 SHEET 2 AA3 5 VAL C 24 GLY C 25 1 O GLY C 25 N VAL A 24 SHEET 3 AA3 5 VAL E 24 GLY E 25 1 O GLY E 25 N VAL C 24 SHEET 4 AA3 5 VAL G 24 GLY G 25 1 O GLY G 25 N VAL E 24 SHEET 5 AA3 5 VAL I 24 GLY I 25 1 O GLY I 25 N VAL G 24 SHEET 1 AA4 5 ALA A 30 VAL A 36 0 SHEET 2 AA4 5 ALA C 30 VAL C 36 1 O MET C 35 N LEU A 34 SHEET 3 AA4 5 ALA E 30 VAL E 36 1 O MET E 35 N LEU C 34 SHEET 4 AA4 5 ALA G 30 VAL G 36 1 O MET G 35 N LEU E 34 SHEET 5 AA4 5 ALA I 30 VAL I 36 1 O MET I 35 N LEU G 34 SHEET 1 AA5 5 VAL A 39 ILE A 41 0 SHEET 2 AA5 5 VAL C 39 ILE C 41 1 O VAL C 40 N ILE A 41 SHEET 3 AA5 5 VAL E 39 ILE E 41 1 O VAL E 40 N ILE C 41 SHEET 4 AA5 5 VAL G 39 ILE G 41 1 O VAL G 40 N ILE E 41 SHEET 5 AA5 5 VAL I 39 ILE I 41 1 O VAL I 40 N ILE G 41 SHEET 1 AA6 5 TYR B 10 HIS B 13 0 SHEET 2 AA6 5 TYR D 10 HIS D 13 1 O HIS D 13 N VAL B 12 SHEET 3 AA6 5 TYR F 10 HIS F 13 1 O HIS F 13 N VAL D 12 SHEET 4 AA6 5 TYR H 10 HIS H 13 1 O HIS H 13 N VAL F 12 SHEET 5 AA6 5 TYR J 10 HIS J 13 1 O HIS J 13 N VAL H 12 SHEET 1 AA7 5 LYS B 16 PHE B 20 0 SHEET 2 AA7 5 LYS D 16 PHE D 20 1 O PHE D 19 N PHE B 20 SHEET 3 AA7 5 LYS F 16 PHE F 20 1 O PHE F 19 N PHE D 20 SHEET 4 AA7 5 LYS H 16 PHE H 20 1 O PHE H 19 N PHE F 20 SHEET 5 AA7 5 LYS J 16 PHE J 20 1 O PHE J 19 N PHE H 20 SHEET 1 AA8 5 VAL B 24 GLY B 25 0 SHEET 2 AA8 5 VAL D 24 GLY D 25 1 O GLY D 25 N VAL B 24 SHEET 3 AA8 5 VAL F 24 GLY F 25 1 O GLY F 25 N VAL D 24 SHEET 4 AA8 5 VAL H 24 GLY H 25 1 O GLY H 25 N VAL F 24 SHEET 5 AA8 5 VAL J 24 GLY J 25 1 O GLY J 25 N VAL H 24 SHEET 1 AA9 5 ALA B 30 VAL B 36 0 SHEET 2 AA9 5 ALA D 30 VAL D 36 1 O MET D 35 N LEU B 34 SHEET 3 AA9 5 ALA F 30 VAL F 36 1 O MET F 35 N LEU D 34 SHEET 4 AA9 5 ALA H 30 VAL H 36 1 O MET H 35 N LEU F 34 SHEET 5 AA9 5 ALA J 30 VAL J 36 1 O MET J 35 N LEU H 34 SHEET 1 AB1 5 VAL B 39 ILE B 41 0 SHEET 2 AB1 5 VAL D 39 ILE D 41 1 O VAL D 40 N ILE B 41 SHEET 3 AB1 5 VAL F 39 ILE F 41 1 O VAL F 40 N ILE D 41 SHEET 4 AB1 5 VAL H 39 ILE H 41 1 O VAL H 40 N ILE F 41 SHEET 5 AB1 5 VAL J 39 ILE J 41 1 O VAL J 40 N ILE H 41 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000